|
| Status |
Public on Aug 08, 2023 |
| Title |
WatR-FLAG strain, input |
| Sample type |
SRA |
| |
|
| Source name |
bacterial culture
|
| Organism |
Methylomonas sp. DH-1 |
| Characteristics |
cell type: bacterial culture
genotype: WatR-FLAG
antibody: none
|
| Treatment protocol |
When the sample reached OD600 ~1.0, final 2.7% concentration of formaldehyde was treated in order to crosslink the protein and DNA for 25 min, and 250 mM of glycin was added to quench the reaction.
|
| Growth protocol |
All samples were cultivated 50 mL of NMS medium in the 500 mL of baffled flask sealed with rubber type screw cap, with the addition of 20% (V/V) methane. The initial OD600 was 0.1 and incubated at 30℃ with shaking of 170 rpm.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed with lysozyme treatment, and the lysate were sonicated, immunoprecipitated with anti-DDDDK antibody. RNase I and proteinase K were treated to eliminate RNA and proteins, and DNA was reverse crosslinked by NaCl with heat treatment. Final DNA eluent were precipitated by phenol-chloroform-isoamylalcohol method. For input, the lysate was directly precipitated.
1 ng of prepared DNA was proceeded to sequencing library construction by using NEBNext Ultra II DNA Library Prep Kit for Illumina (#E7645, NEB) following manufacturer's instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
WatR-IP
No antibody used for input.
|
| Data processing |
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with default parameter.
Cleaned reads were mapped to reference genome using bowtie2 with default parameter.
Peak calling was performed by findpeaks command in homer v. 4.10.3 using "-style factor" parameter.
Resulted peaks were annotated by annotatePeaks.pl in homer package.
Peaks was transformed to bed file using pos2bed.pl in homer package for detailed analysis.
Assembly: Methylomonas sp. DH-1 (GCF_001644685.1)
Supplementary files format and content: bigWig, the graph represents normalized reads per million of mapped reads
|
| |
|
| Submission date |
Jun 15, 2022 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Yong-Joon Cho |
| Organization name |
Seoul National University
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL32357 |
| Series (2) |
| GSE206216 |
Determination of WatR binding site in Methylomonas sp. DH-1 after lactate adaptive evolution |
| GSE206217 |
Regulation of acetate tolerance by unannotated small open reading frame (smORF) polypeptides in Methylomonas sp. DH-1 |
|
| Relations |
| BioSample |
SAMN29111891 |
| SRA |
SRX15714216 |
